[phenixbb] problem with a twinned data set

Paul Adams PDAdams at lbl.gov
Sat Mar 1 17:06:05 PST 2008


Hi Pascal,

   the reason CNS tells you that there are no twin laws is that it  
only considers true merohedral twinning and not pseudo-merohedral -  
the latter is what xtriage is reporting.

   Cheers,
	Paul

On Mar 1, 2008, at 4:04 PM, Pascal EGEA wrote:

> Hi All
>
> This a question of  general Crystallography and use of Phenix to  
> deal with twinned data.
>
> I am having difficulties with a data set. We have data (2.6 ang  
> resolution) that can be scaled and reduced in P222 with a Rmerge of  
> 7%, the systematic absences show a screw axis ( it is P22(1)2).
> However MR in Phaser failed in this orthorhombic settings when  
> searching for  2 molecules of the  complex in the AU.
> If we reduce and scale the data in P2(1) and look at the  
> diffraction pattern in HKLVIEW there is  a /mmm symmetry. In the  
> monoclinic P2(1) setting we can find 4 molecules of the complex (by  
> MR in Phaser) and can refine it with Phenix  to a Rfac/Rfree of 28%/ 
> 34%. 2 molecules have good electron density whereas the two other  
> ones have one of their domain very poorly defined in density. This  
> is looking very suspicious to me and I am wondering if this refined  
> structure is partially wrong?
>
> Meanwhile  I used phenix.triage on the data processed in P222 and I  
> am confused with the output.
>
> ##----------------------------------------------------##
> ##                   Twinning Analyses                ##
> ##----------------------------------------------------##
>
> Using data between 10.00 to 3.36 Angstrom.
>
> Determining possible twin laws.
>
> The following twin laws have been found:
>
> ---------------------------------------------------------------------- 
> ---------
> | Type | Axis   | R metric (%) | delta (le Page) | delta (Lebedev)  
> | Twin law |
> ---------------------------------------------------------------------- 
> ---------
> |  PM  | 4-fold | 2.851        | 0.000           | 0.013            
> | -l,k,h   |
> ---------------------------------------------------------------------- 
> ---------
> M:  Merohedral twin law
> PM: Pseudomerohedral twin law
>
>   0 merohedral twin operators found
>   1 pseudo-merohedral twin operators found
> In total,   1 twin operator were found
>
>
> ---------------------------------------------
>  Analysing possible twin law :  -l,k,h
> ---------------------------------------------
>
> Results of the H-test on acentric data:
>
>  (Only 50.0% of the strongest twin pairs were used)
>
> mean |H| : 0.368   (0.50: untwinned; 0.0: 50% twinned)
> mean H^2 : 0.194   (0.33: untwinned; 0.0: 50% twinned)
> Estimation of twin fraction via mean |H|: 0.132
> Estimation of twin fraction via cum. dist. of H: 0.115
>
> Britton analyses
>
>   Extrapolation performed on  0.14 < alpha < 0.495
>   Estimated twin fraction: 0.127
>   Correlation: 0.9955
>
>
> By comparison if I run the detect_twin routine of CNS it tells me  
> that they are no merohedral twin laws for the point group 222  
> (using the statistical method of Yeates) ? This is  confusing me  
> quite a bit.
>
>
> Assuming that the twinning law suggested by Phenix is correct how  
> should I proceed?
> I have noticed the section concerning refinement using twinned data  
> in Phenix
> phenix.refine data.hkl model.pdb twin_law="-k,-h,-l"  
> detwin.map_types.aniso_correct=true
>
> but It seems I  only have a MR solution in P2(1) but not in P222(1)  
> so how can I refine in P222(1)
>
> I will greatly appreciate your input, many thanks.
>
>
> Pascal F. Egea, PhD
> University of California San Francisco
> Department of Biophysics and Biochemistry
> Robert Stroud Laboratory
> pascal at msg.ucsf.edu
>
>
>
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> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

-- 
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
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BLDG 64R0121
Berkeley, CA 94720, USA.
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